The Midnight Birds
by legendoflaura
Summary: Contains spoilers for Agents of S.H.I.E.L.D. Season 2. Jemma Simmons leaves without a trace while Fitz is still in a coma. The rest of the team has a lot on their plate and trying to cope with their present predicaments. In the meantime, what is Jemma Simmons up to?
1. Chapter 1

1

Coulson found her where he expected her to be- inside her bunk packing her bags. He leaned against the doorframe, arms and legs crossed and waited until she noticed the hair raising sensation of eyes on her back.

"I didn't think you'd be leaving so soon," Coulson said as she turned to look at him. His voice carried his trademark calmness.

"Well, there's no use standing bedside vigil, Fitz will wake up soon," Jemma Simmons replied. Her hair was swept up in a ponytail. The scratches on her face were only a couple days old.

"Are you going to say good-bye?" Coulson followed up. He untangled his limbs and moved into the room, stopping to stand over Simmons.

Simmons zippered the bag she had been chucking belongings into. She slid the bag under her bed and stood up to face Coulson. Her chest rose and fell vigorously, a telltale sign of nerves. She wagered for a brief moment of telling the rest of the team she had to leave. First would come the protestations, Skye would be at the forefront of the polemical pleas. Next she'd be bombarded with questions. It would be throwing caution to the wind if she answered any of them. It would be simpler to flee in the night then give some completely untrue answers.

"I wish I could, Sir," she replied to Coulson.

"Well in that case," Coulson said wrapping his arms around Jemma, "let me say good-bye now. But please, visit Fitz before you go and talk to him. He'll hear you."

"It's a promise, Sir."

After the unofficial goodbye, Simmons followed Coulson out of the room to the kitchen. She helped with meal prep and clean up like usual, sat down and had a beer with Skye and Triplett after. She bid them goodnight like always and returned to her bunk in the Playground for the last time. She holed up there for a few hours, double-checking her luggage. She contemplated writing a brief note to the rest of the team but decided against it. Once she was sure everyone had gone to sleep, Jemma gathered up her luggage and headed down to the medical bay. She left her luggage outside of Fitz' room. The lights were on, but dim, casting a yellow glow over his sleeping body. For a time he had been in an induced coma, but now it was all on his own to wake up. His arm was in a proper sling but his face still bore remnants of the plunge into the ocean.

Jemma quietly entered the room, her footsteps barely audible over the buzzing of machines and the light breaths emanating from the gurney. She took the seat next to his bedside and sat on the edge of it, leaning forward. Her hand took the hand of his uninjured arm. It was cold.

"Oh, Fitz," she said pitifully.

"I don't think you'll hear me Fitz, but, I wish I could tell you why I have to leave. You're going to wake up and I won't be there for you," Simmons said softly, she was looking into his face, deeply focused.

"I-I won't be there, physically. But I want you to know you will never leave me, and I hope you'd keep me in your mind as you do in your heart. Thank you for being with me this whole time, Fitz…"

Jemma's voice trailed off because it began to succumb to the pressure of tears. It would be the last time she would cry for a long time.

She stood up and leaned over Fitz and placed a kiss on his forehead. She pulled his blanket up to his chin to keep him warm and crossed the room to exit. At the doorframe, Jemma lingered, and gazed at Leopold Fitz one last time before her departure.

Coulson had known she needed to leave when things had taken a bad turn. Jemma knew he was the only person she could trust to help her leave without making a scene or a trace. Using an old electromagnetic pulse she was able to disable the alarm systems on one of the Playground's few entrances. She slipped out quickly, only having a moment before the system would reboot and alert the inhabitants.

Jemma was several miles down the road, veiled in the achromatic night. Fitz, perhaps subconsciously sensing her presence in the room before, opened his eyes, propped the top half of his body up on his elbows and whispered into the darkness one single word.

_Jemma._


	2. Chapter 2

2

Melinda May was the first one awake the next morning. She was almost done with her session of tai chi when Coulson strolled in. While Coulson never slept much he always appeared calm. This morning she could sense the agitation in his pace. Something was amiss.

"Phil, do you need to vent?" May questioned. Recently Coulson experienced such pent up distress he would stay up all night inscribing the walls with the strange drawings. May would stick with him, photographing the glyphs and bringing him a cup of tea when his wrist would finally give out and he would snap out of thick concentration. This morning felt like it would be one of those days.

Coulson brushed it off, telling May he'd make it to tonight and had much to do. Koenig brought him breakfast and Coulson did what he had been doing almost every day since Hydra's resurgence; shutting himself in his office for hours.

When Skye woke up, she dressed in her workout clothes, grabbed a cup of coffee and two bowls of oatmeal and trotted down to the medical bay to visit Fitz and Simmons. Jemma had been there the whole week from early in the morning and any free moment of the day she had. Routinely, Skye joined in the morning and brought Jemma breakfast. Skye would try and supply jokes and lightheartedness since Jemma needed the cheering up.

This morning, Skye walked into the room with an empty chair next to Fitz' bed. It was peculiar, but Skye brushed it off thinking Jemma might be in the shower or just late getting up. She had been staying up long nights.

Skye placed one of the bowls on the table nearest to Fitz' bedside and casually slunk down in the chair in the corner.

"So, Fitz, did you have any good dreams last night?" Skye did her best to keep the atmosphere light and airy despite not having another person to bounce these kinds of statements off of.

She began eating her oatmeal and occasionally waxing poetic on small talk. Still, even after ten minutes of Skye trying to preoccupy the static air, Jemma did not come waltzing in with her characteristically apologetic British composure.

Always intuitive, Skye began to question the abnormal morning. She shot back up onto her two feet and started to snoop around the room. Skye barely knew the proper way to care for a mild burn but sticking around Fitz' hospital room for the week taught her a couple things about vital signs.

"Fitz," Skye whispered, staring at a screen. "You woke up."

The next step was to find Simmons. Maybe Jemma already knew Fitz was out of his coma and went to tell Coulson.

On her way to Coulson's office, Skye bumped into May. Bursting with excitement over the good news, Skye informed May about Fitz' consciousness.

"Was Jemma telling Coulson? She wasn't in the room with Fitz so I assumed she was letting him know," Skye babbled on.

May had just come with her morning chat with Coulson so she knew this wasn't true. In her stoic and silent manner, May delicately shook her head. Skye looked away from her trying to process the information, she took off to Jemma's bunk.

At first the room seemed normal. The bed was made according to Jemma's pristine standards. Skye slowly stepped in. She had hoped Jemma was sleeping in late. Skye walked up to the bed and sat down. Jemma was a predictable person, a creature of habit. Skye was going to have to think harder on where she must be.

But the answer was already starting to piece itself together in the back of Skye's mind. On Jemma's bureau usually sat a picture of her and her parents. That was missing. And so was a hairbrush. Skye walked open to the closet and opened the door. It was just empty hangars. Jemma was gone.

It had been a very long night for Jemma Simmons. She had to do most of her traveling during the dark hours, and by the time morning rolled around she was on a flight.

Slightly disoriented from the long travel, Jemma stepped off the plane, collected her luggage and proceeded through customs. On the other side, a man in sunglasses and a suit stood with a sign of her name. He was tall, young, and had dashingly good looks. He may have looked the part of all the other chauffeur's picking up their passengers but he was far, far from normal.


	3. Chapter 3

3

"_Roman_," Jemma said curtly.

The man in the suit continued smiling and extended an arm to hold Jemma's waist as she came close to him.

"Ms. Simmons!" he exclaimed. Jemma tried to shift out of his light grip but with all her luggage she couldn't move easily. Discomfort splashed across her face.

"It's Dr. Simmons, actually, Roman," she interjected.

With the hand not on her waist, the one with the sign still in its clutch, Roman extended it to the exit of the airport. Jemma turned away from looking at him and made her way to the exit. Roman followed next to her and took a few of her bags.

"I thought someone else was picking me up," Jemma said as she crossed through the open sliding door.

"Well you thought wrong," he replied, they were crossing the streets to the parking lot.

Jemma was exhausted. Leaving the Playground had been taxing on her body and mind. She couldn't look back now. There were people that needed her more than Fitz needed her and now she needed to look towards that direction.

"Well, _Ms. Simmons,_ plans changed. You will see the people you came here to see. Eventually. Today I have a much more important agenda for you to comply with. Here's the first lesson: from now on don't be caught without a smile on your face," Roman said. Jemma shuddered at the incorrect title he was becoming consistent on using.

"It's _Doct-," _Jemma began to huff.

"Ah-uh-uh, you're not smiling," Roman interjected this time.

Roman unlocked a black SUV and started to load Jemma's luggage into the trunk. Jemma stood to the side watching with her arms folded. She defied Roman's instructions by scowling.

Roman slammed the trunk door particularly hard. He snuck his hand into his pocket and pulled out a cell phone to which he tapped on the screen. He swiftly moved right in front of Jemma, inches from her face but with just enough room to show the screen of the phone to her.

"This, this is why you will be smiling_, Ms. Simmons_. Because the life of these two people_ depend_ on it," Roman sneered. His voice was abrasive, the professional and cool manner he had before had been replaced with mania.

After staring into Roman's eyes as he delivered his chilling message, she focused her eyes on to the screen. Two older people were blindfolded and hog-tied. An agent dressed in black head to toe held a rather large weapon at attention. It was a livestream video. Jemma knew immediately who they were, and fighting back the tears pinching at the sides of her eyes in reaction, Jemma upturned the corners of her mouth into a shaky and superficial smile.

Recoiling and softening up his tough gaze, Roman nudged Simmons to the passenger side of the vehicle while he climbed into the driver's side.

"See? Smiling isn't so hard, you'll get used to it," Roman said calmly.

"I thought the conditions of this arrangement were based upon them remaining unharmed," Jemma said alluding to the couple in the video.

"Hydra has to ensure that you are with them, and now you know if you step out of line there are consequences that won't just affect you," he responded.

Other than the radio it was a quiet drive after that brief conversation. For some time Jemma watched the trees and little towns fly past the window. Every time she'd see her smile fading in the windows reflection she corrected herself. It was a cycle until she eventually passed out from exhaustion.

When she awoke, Roman was pulling the SUV into a quiet suburban apartment complex.

"Welcome to your new home, Ms. Simmons."

With a smile resurfacing on her face from her nap, Jemma corrected Roman's misspeak in her head, _Doctor Simmons._


	4. Chapter 4

_- Author side note: I am so, so sorry it took so long to update. Last weekend I attended New York Comic Con and the rest of the week was spent getting my life in order/dinner parties/AOS watching/hiking/other random things you don't need to care about! But here's chapter 4! -_

4

Fitz woke with a shiver. Although the room was dimly lit, the light still made his eyes squint. It had been more than week since they were last open. He was alone.

His consciousness sent the sensors off. Fitz was lost on what to do; he was disoriented, confused, and exhausted. He was taking large gasping breaths because for some reason he felt he hadn't been able to breathe.

And Jemma.

His mind went straight to the thought of her as if she was the only thing he could ever think about.

Fitz couldn't quite remember why at this moment it was so imperative to see her safe and alive. He just wanted to know she had a heartbeat. Her voice kept echoing inside the confines of his head but he couldn't make out any words.

The first person to enter into Fitz' medical room wasn't a doctor, but Coulson. While the man bore a relieved facial expression, Fitz stared back looking horrified.

"Hello Fitz, how are you feeling?" Coulson said, coolly.

Fitz wanted to speak but the words just didn't appear in his mind. His bottom lip quivered and he looked up at Coulson with befuddlement in his eyes. Coulson sensing now that Fitz couldn't reciprocate a conversation, sat down at the edge of Fitz' bed.

Coulson was always even-tempered, even angry or in a period where most would panic he had control. It was what made him a good leader. But what made him a great leader was just Coulson sitting on the bed with Fitz, prattling off about some of the mundane things Fitz missed while in a coma.

Coulson's one-sided talk lasted for a couple of minutes. Fitz wasn't so much as listening as he was just hearing. The familiar sound of footsteps racing down a hallway caught Fitz' attention to the point where he snapped his head to the doorway. Before the visitor turned the corner into the room, Fitz said the first word his conscious brain could form.

"Jemma?"

His voice was low and raspy, unused and unfamiliar with the exact way the muscles in his throat were supposed to contract to form sounds. His attempt, a croak, delighted Coulson for a moment until he realized how difficult it would be to tell Fitz she wasn't there.

Saved for the moment, the pair of footsteps in the hallway belonged to two people. Skye and Triplett appeared in the doorframe moments after Fitz' vocal breakthrough. Skye crossed the room in a millisecond and threw her arms around Fitz. In return, he stiffened; shocked and melancholic this wasn't from someone else. Tripp followed Skye in, walking slowly over to the bed. After Skye recoiled from the hug, Tripp gave him a congratulatory squeeze on his shoulder.

Then, a voice from the corner of the room piped up. He hadn't seen or heard her come in. But she was there.

"Oh, Fitz! Look everyone is coming to see you. Isn't that wonderful?" Jemma said cheerfully.

Fitz did more than just look at her. He gazed at her like he was seeing the Large Hadron Collider for the first time. His body was washed over with a sensation of warmth. Everyone in the room was ignoring her, but she was the center for him.


	5. Chapter 5

5

Jemma could not fall asleep the first night in the apartment. She stared at her alarm clock, the same one she had in her room in the Bus and at the Playground. Maybe it was the yellow colored walls that were a vast change from the typical black and grey SHIELD color scheme. A little after midnight, Jemma picked herself off the freshly made sheets. This wasn't home to her, but she had act like it was.

The apartment made an entirely different spectrum of noises then her previous habitats. She could hear water run through the pipes when her neighbor ran the kitchen sink. A family of birds lived in the tree outside of living room window; she could hear them shuffle in and out of the leaves. She was so used to seeing open sky and clouds from the view of the Bus.

Jemma couldn't remember the last time she had a good sleep. It had to have been before the Insight events in D.C. She had stayed up most nights worrying over Fitz or just plain worrying. She would sit in the kitchen of the playground and make tea over and over again. Drinking only half the cup she knew it was wasteful, but that had been the only way to soothe her running mind.

Coulson would walk into the kitchen almost all of those nights that he was at the Playground. He'd sit with her and have a cup discussing what they both new would need to happen. Coulson just didn't know how soon she needed to leave.

There were two people in the world that depended on Jemma Simmons. Coulson knew from day one he met Jemma that they would always be her priority. Soon after Fury had fished Fitz and her out of the ocean, Coulson set up a secure line for Jemma to make her important phone call.

Roman's voice was at the other end of the call. She expected it, but wasn't happy about it.

"A week," he said.

Jemma wasn't sure if Fitz would be out of her coma by then but she had no choice.

With her pantry empty, Jemma looked to the phonebook the landlord had handed her. She called a cab and asked the driver to take her to any convenience store that might be open at this late hour. Good thing 7-11's were plentiful in suburban America.

Jemma asked the taxi driver to wait for her. Hanging outside of the store were a bunch of teenagers, knocking back sips of energy drinks and fiddling with their skateboard wheels. One of them beckoned Jemma to buy them alcohol.

"Sorry boys, not tonight," Jemma sailed past them into the store.

She scanned the aisles of junk food until she spotted a few boxes of tea. She piled Earl Grey and green tea into her arms, grabbed a carton of milk and checked out at the register. She put her groceries in the back of the cab but asked him for another moment. She ran back to the store and asked if she could use the store's phone. She made up some emergency. The clerk obliged, perhaps because of her English charm, perhaps because he was bored and she was harmless.

She called a number she had memorized on the plane ride, praying it would be picked up.

"Glad to hear you got the number right," Coulson's voice came over.

Jemma sighed with relief, her back against the break room's wall, her free hand cupping her forehead.

"Oh, Sir, so glad I got ahold of you. I have news for you," she said, trying to make the call quick despite wanting to stay on the line forever.

"Shoot," he said. She knew he didn't have all the time in the world either.

"Roman is going to have me work as a scientist for Hydra…I-I don't know if I can do it," she gushed.

"This can put us at an advantage, you know you have no choice in doing this, you're going to have to do it. Just forget for the moment who they are and do your job, do science. I have news for you as well, this may make it easier for you, would you like to hear it?" Coulson responded.

"Of course," Jemma replied.

"Fitz woke up today. I'm not sure he understands yet if you're gone or not, he's very confused. But he'll be better now. Call me again tomorrow form a secure location so we can set up dead-drops. Goodnight," Coulson finished.

"Thank you, sir. And good night to you too," she responded.

"One more thing, don't forget to get some sleep."


	6. Chapter 6

_Hello everyone! The delay was due to my busy week, I attended a concert and started a new writing gig and just got wrapped up in my work. Thank you for the messages and follows! You are all so sweet. This chapter is kind of interesting and will be back on track in the next one to the present! Enjoy! _

_[and p.s I'm not British so I may not get the dialogue correct, sorry!]_

6

Jemma Simmons was enjoying a breezy summer day by rocking back and forth lazily on the swing her father had put up on the willow tree overlooking the pond. Their yard was lovely, the typical bucolic English countryside oasis everyone outside of England pictured when they thought of England's rural areas.

Akin to the house was their small farm and livestock paddock. Jemma had spent all morning assisting the veterinarian checking up on the animals. The veterinarian was new, as the previous veterinarian who looked after her family's stock had just passed away. This new veterinarian, Dr. Provost, was around the same age as her parents and had just moved to town with his young family. He was vastly intrigued by Jemma's intelligence, that such a young girl was diagnosing the animals alongside him.

"I may have to bring my Roman around here, she may be a good influence for him," Dr. Provost joked to Jemma's father.

Jemma's father smiled, beaming at his daughter who was looking deep into the ears of a cow with an ear infection.

"She's gets it all from her Mum. Say, Jemma could use a playmate, bring your boy around anytime," her father replied. The two men made plans to have tea later and introduce their children.

Jemma was now on the swing waiting for the doctor and his son to arrive. She was homeschooled and at this point hadn't met many children her age. She was nervous, but confident, she had never known any difference.

Soon her mother's voice rang out into the air, calling her in for tea and biscuits. Jemma kicked her feet back and forth gaining momentum on the swing until at the optimal point she jumped off. She rang into the house, her pigtails flying behind her.

"Hello, Mum!" Jemma said cheerfully. She immediately went to wash her hands in the kitchen sink. Jemma's mother was setting pastries on the table. There were voices coming from the front of the house, Dr. Provost and his son has just arrived it seemed.

Jemma assisted her mother with the last few touches to the table and sat down just as her father entered with their guests. Mrs. Simmons gushed over the little boy standing at Dr. Provost's heels. He had unruly blonde hair and a kind of smile that Jemma could only describe much later in her life as devilish.

After being introduced and having their teas, the parents ushered the children outside to play while they talk shop.

Roman and Jemma raced to the swing, Jemma getting their first having known the way of the land better.

Roman, bitter, shoved her off the swing and jumped on top of it.

"You'll never win against me!" he proudly touted as Jemma looked up from the ground. Jemma didn't cry. She got back on to her two feet, brushed herself off and realized Roman would be a good friend for her to have.

"Do you like gross things, Roman?" Jemma asked.

"What do you know about gross things?" he huffed, a tinge of arrogance in his voice.

"I've been dissecting a squirrel in my mum's lab, would you like to see it Roman?"

Roman followed her back to the garage-like building close to the house. Computers and all sorts of machinery and science instruments lined every tabletop and shelf.

Jemma brought him into a smaller side room; they were greeted by the smell of decomposition and embalming liquids. Roman gagged.

From that point on, and many years to come, Roman would be by her side, fascinated by the little girl who had a firm grip on a scalpel and a thirst for adventure.


	7. Chapter 7

_I'm participating in NaNoWriMo this month so I may not get much writing for this fic done. As it is I'm running way behind on my Nano and it's only day 4. Please send me good vibes! - L_

7

Leo Fitz thought some elaborate joke was being played on him. Coulson had told him Jemma was gone, she left, she went to be with her family. But she was in the room with them. Fitz wanted to laugh thinking they were still trying to prank him after all this time. Maybe they thought it would lighten the mood. Either way, Fitz pretended to go along with them, see how long they could keep it up. Maybe they figured it would be better for his health.

In a few short days, Fitz returned to his room. It felt nice to recover in privacy for once. Of course, Jemma spent all her time sitting on his bed or reading in the corner. She insisted in keeping him company. It was nice to have her around constantly; it meant she cared for him.

Jemma was a bit strange with all things considering. Fitz had limited mobility and was often left out of team meetings or assignments due to his broken arm. But Jemma wasn't going to them either, and she wouldn't even make him tea like they used to together. He even snuck down to the kitchen one night to make some tea for the both of them but hers remained untouched.

He was itching to get back to work, to not feel useless. He understood what a critical time it was for the team. Everything had broken apart and the team was suffering. They had limited resources and limited people. Fitz knew his role was important. About a week after waking up he headed back to the lab. Jemma followed.

However, Jemma hovered over him. He asked if she had any work to get done and she told him she didn't, and that's why she was able to help him. She was a great help for him in the lab. Where his mind fluttered in remembering terms and had difficulty connecting related objects, Jemma filled him in. She was patient with him. Perhaps her only assignment was aiding him on recovering. Coulson had explained that his lack of oxygen had resulted in hypoxia.

Skye, Tripp, and May were around the most. Coulson was always away and when he wasn't away, he was locked inside his office. Skye tried to talk to Fitz but their conversations fizzled. She bit her lip constantly and kept shifting whenever she was near him. She couldn't look him directly in the eyes. It made him feel like there was something seriously wrong with him. He merely couldn't string words together, that's all. That wasn't something too bad. But here Skye made his presence seem like it was a problem. Like he was constantly doing something wrong. Tripp would pass by every so often to say hello or bring him a snack. Fitz recalled before the accident becoming closer to Tripp. And now it seemed they were back to a casual work relationship. The only positive was Jemma wasn't hanging off him every two seconds. May at least would come and listen to him. She was a lot warmer then she used to be, and he thought about how nice it was to see this softer side of May.

One day, Coulson appeared with a group of agents and new recruits. While many of them would be working in the lab as medical technicians, Alphonso Mackenzie was a mechanic and would be sharing some of Fitz' space and engineering tools.

Jemma reminded Fitz to play it cool around him, that Mack may not be comfortable with Fitz' stuttering. It was at this point, getting worse. He assumed it was due to nerves. Jemma wouldn't say what it was. Some biologist she was.

Fitz didn't really feel anything was wrong. He was getting frustrated with his inability to speak to the same caliber he did. And he could surely do without the constant shaking and the perpetual ache in the arm he had broken, but otherwise he was alive and functioning.

About the second week after Fitz' recovery, things started to turn for him. Coulson came and gave hi his first assignment, to get the cloaking device working. Fitz accepted, he used to always tinker around with the cloaking and shouldn't have had a problem.

Coulson was just about to lave the room, disappear off into another assignment or something where he would be away from the base for days. Fitz stopped him, and seeing that Jemma was out of the room for a moment, he wanted to bring up a concern he had about her. That she should be helping with the work for the medical team. A lot of people were still recovering from their injuries. And Coulson had a reply for him that would confound him.

"Fitz, we told you this before, Jemma isn't here," Coulson said, softly.

Fitz bit his lip. Yes, she was here. The rest of the team needed to stop with the charade. It wasn't funny anymore.

"Sir, she's been here the whole time, helping me get better," Fitz replied.

Coulson looked at Fitz with sternly but his eyes were telltale signs of sadness.

"No, Fitz. She's been gone since the day you woke up."

Coulson wanted to continue, to tell him he wasn't getting any better, but he felt that was enough heartbreak for Fitz to endure in one day.


End file.
